The Confederation was an alliance of systems that joined Corellia in her revolt against the Galactic Federation of Free Alliances from 40 ABY until at least 43 ABY. The Confederates portrayed themselves as freedom fighters while the Alliance, especially Jacen Solo, labeled them as terrorists. The rebel movement was eventually defeated by the Galactic Alliance and forced to surrender in the last battle of the war. However, following the death of Darth Caedus, it took part in peace talks proposed by the Jedi Coalition. After the war the Confederation remained an independent government and emerged as one of the three major galactic powers, alongside the Galactic Alliance and Imperial Remnant.

As Jacen Solo, now the Sith Lord Darth Caedus, seized control of the Alliance, the galaxy finally erupted into a state of total war. The combined fleets of Corellia, Bothawui, Hutt Space, and Commenor engaged with Core World forces, hoping for a decisive battle with the forces of Coruscant. Although Balmorra quickly fell to the Confederation, the main assault force was eventually defeated at Kuat, and the failure of getting the Wookiees to join with them after the Battle of Kashyyyk left them out on a limb. However, the Alliance in turn suffered a major setback when the New Jedi Order, unwilling to further support Caedus, withdrew at Kuat and formed the Jedi Coalition.[6]

Over the following weeks, the Confederation was weakened by one defeat after another. The forces of Commenor and Bothawui were severely depleted by Alliance attacks, Centerpoint Station was destroyed by the Jedi and their allies, and eventually Fondor fell as well, during which Caedus won support of the Imperial Remnant. The tide had turned against the Confederation.[5][7][8]

The final stand of the Confederation was its participation in the Second Battle of Roche, along with the Jedi Coalition and the Alliance-in-exile. However, their fleets were trapped in the Roche system by Admiral Nek Bwua'tu and badly beaten. Darth Caedus, now more obsessed with defeating the Jedi than ever, left matters at Roche to Bwua'tu while he took a joint-Alliance/Imperial force to Shedu Maad, only to perish in the ensuing battle.[9]. With Caedus dead, the forces under his command aligned themselves with the Coalition. The combined might of the Jedi, the Alliance, and the Remnant forced the Confederation to surrender, ending the war. Despite this, the Confederation refused to rejoin the Alliance, but did take part in the Unification Summit on Coruscant in 43 ABY. What became of the Confederation after this is unknown, but it is clear that it had completely rejoined with the Alliance at some point prior to the Sith–Imperial War.

The Confederation Fleet managed to inflict heavy losses against enemy forces, but its resources were very depleted near the end of the war. When Jedi Coalition decided to reconstruct the Galactic Alliance with the help of Imperial Remnant, after the death of Darth Caedus, the Confederation was forced to surrender and sit down to negotiate with the victorious side.

During its existence as the Corellian Confederation, the secessionist government was headed by the Five World Prime Minister, although this office briefly changed to the President of Five Worlds. When its membership grew beyond the Corellian sector, the Confederation had no single Head of State, because its leadership consisted of political leaders and military commanders of individual planets, organizations and factions, though the Prime Minister of the Five Worlds retained much power and often spoke in the name of the Confederation. Therefore its policy was inconsistent - some members differed in terms of method of warfare and had various ideas on how to win the Second Galactic Civil War. However, the Confederation was known by close economical and military cooperation. To better coordinate military strategy and provide many fleets a single, united command, the office of the Supreme Commander of the Confederation Fleet was created. Later, the Supreme Commander virtually assumed the powers of head of state and after the war represented the Confederation at the Unification Summit.

The staunch enemy of the Confederation was the Galactic Federation of Free Alliances, assisted by the Imperial Remnant. It also opposed the Hapes Consortium when Queen MotherTenel Ka Djo was loyal to the GA government based on Coruscant, but later Confederacy leaders concluded a pact of neutrality with the Consortium. The Jedi Coalition was its co-belligerent; both factions fought the GA mostly independently of each other, though they shared intelligence about maneuvers and targets of their common enemy. When the Galactic Alliance split into two factions, one of the Confederation founders, Fondor, offered safe refuge to forces loyal to Cha Niathal and permitted them to use the planet to set up a government-in-exile, seeing in Jacen Solo, the current GA Chief of State, the greatest threat to all. The Confederation managed to find some powerful allies such as the Heritage Council and Hutts, while establishing trade contacts with the weapons-producing Mandalorians. It also tried to increase its forces in various ways like planning a political coup on Hapes, or offering assistance to endangered planets such as Kashyyyk.

The main goal of the separatist's government was to liberate itself from the yoke of the strongly centralized and very restrictive Galactic Alliance, represented particularly in the person of Jacen Solo/Darth Caedus, a colonel of the oppressive secret police Galactic Alliance Guard and later Galactic Alliance Chief of State. Though some members of the Confederation saw a better future in the full independence of GA, others united under its banner, looking for opportunities to rule the galaxy by fear and force their potential enemies to obedience, for example by threatening to use superweapons like the Centerpoint Station.